The third-seeded Indian pair won 6-3, 5-7, 11-9 to set up a clash with second seeds Max Mirnyi and Daniel Nestor, who defeated fourth seeded Jurgen Melzer and Philipp Petzschner 6-4, 6-1 in their semifinal match.
Bhupathi and Paes led 6-3 2-0 before Marach and Tipsarevic turned things around to even the match at one set all.
"We let our lead slide. It got tight, down match point, but Leander and I have been in the situation before and continued to work for each point," Bhupathi conceded.
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The Austrian-Serbian combination had a match point at 9-8 in the tie-break but lost the final three points to crash out.
The final is a rematch of the semifinal clash at the Australian Open, in which Paes and Bhupathi were triumphant in three grinding sets.
